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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
IPO4 ENST00000354464 39.00 47.36 41.37 0.90 0.66 0.73 1.75 2.01 2.03
TMEM127 ENST00000258439 39.01 63.48 50.27 0.90 0.49 0.65 1.76 1.25 1.92
MNT ENST00000174618 39.01 3.87 19.44 0.90 3.30 1.53 1.76 0.31 0.84
CALD1 ENST00000361675 39.02 9.54 22.44 0.90 2.51 1.16 1.76 0.49 0.97
RNF114 ENST00000244061 39.02 42.01 38.80 0.90 0.59 0.82 1.75 1.84 2.03
MTMR11 ENST00000439741 39.03 59.98 48.35 0.90 0.53 0.67 1.75 1.37 1.88
ENDOG ENST00000372642 39.03 84.33 62.55 0.90 0.28 0.48 1.75 0.44 1.40
ENG ENST00000373203 39.04 8.21 21.77 0.90 2.57 1.25 1.75 0.45 0.93
MYL3 ENST00000395869 39.04 49.99 42.82 0.90 0.66 0.68 1.75 2.02 2.01
CLCN6 ENST00000346436 39.05 31.73 33.55 0.90 0.95 0.87 1.76 1.47 1.72
CNGA1 ENST00000402813 39.05 50.36 43.07 0.90 0.66 0.66 1.76 1.96 2.01
SFTPC ENST00000318561 39.06 69.02 53.45 0.90 0.54 0.62 1.76 1.15 1.83
SCD5 ENST00000319540 39.06 51.73 43.74 0.90 0.61 0.61 1.77 1.88 2.02
LAMA3 ENST00000313654 39.07 34.70 35.07 0.90 0.80 0.86 1.77 1.54 1.75
FGB ENST00000302068 39.07 20.77 28.11 0.90 1.44 0.81 1.77 0.81 1.28
SYNE2 ENST00000358025 39.08 16.15 25.69 0.90 1.82 1.05 1.77 0.69 1.22
LTBP4 ENST00000308370 39.08 12.79 23.99 0.90 2.07 1.09 1.77 0.59 1.05
RAB3GAP2 ENST00000358951 39.09 10.01 22.72 0.90 2.35 1.18 1.77 0.49 0.98
HDAC6 ENST00000334136 39.09 0.44 17.67 0.90 4.12 1.66 1.77 0.28 0.78
CAPN15 ENST00000219611 39.10 13.18 24.16 0.90 2.04 1.11 1.77 0.60 1.05
DDR1 ENST00000376575 39.10 29.77 32.64 0.90 1.13 0.87 1.77 1.40 1.63
SYPL1 ENST00000011473 39.11 43.78 39.80 0.90 0.61 0.80 1.77 1.96 2.02
RNF180 ENST00000389100 39.11 46.50 41.02 0.90 0.73 0.76 1.77 2.02 2.04
IQGAP2 ENST00000274364 39.12 41.12 38.44 0.90 0.59 0.84 1.77 1.82 2.04
TGDS ENST00000261296 39.13 62.25 49.62 0.90 0.53 0.67 1.77 1.34 1.84

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